h5dump problem with compound type containing vlen...

• To: netcdf-hdf@xxxxxxxxxxxxxxxx
• Subject: h5dump problem with compound type containing vlen...
• From: Ed Hartnett <ed@xxxxxxxxxxxxxxxx>
• Date: Tue, 06 Sep 2005 12:35:39 -0600

Howdy HDF5 folk!

Using a recent version of HDF5 from cvs, I encountered the following
output from h5dump:

HDF5 "tst_h_vl.h5" {
GROUP "/" {
   GROUP "grp1" {
      DATASET "sea_sounding_dataset" {
         DATATYPE  "/grp1/sea_sounding_type"
         DATASPACE  SIMPLE { ( 3 ) / ( 3 ) }
         DATA {
            h5dump error: unable to print data
         }
      }
      DATATYPE "sea_sounding_type" H5T_COMPOUND {
         H5T_STD_I32LE "sounding_no";
         H5T_VLEN { H5T_IEEE_F32LE} "temp_vl";
      }
   }
}
}

The program that produces the file is here (note that it is the second
file produced which created the file that h5dump can't handle:

/* This is part of the netCDF package.  Copyright 2005 University
   Corporation for Atmospheric Research/Unidata See COPYRIGHT file for
   conditions of use.

   This program excersizes HDF5 variable length array code.

   $Id: tst_h_vl.c,v 1.3 2005/08/11 15:39:57 ed Exp $
*/
#include "tests.h"

#define FILE_NAME "tst_h_vl.h5"
#define DIM1_LEN 3
#define ATT_NAME "att_name"

int
main()
{
   hid_t fileid, grpid, spaceid, typeid, attid;
   hsize_t dims[1] = {DIM1_LEN};
   hvl_t data[DIM1_LEN];
   int *phoney;
   int i, j;
   size_t size;

   /* Create some phoney data, an array of struct s1, which holds a
    * pointer to a variable length array of int. */
   for (i=0; i<DIM1_LEN; i++)
   {
      if (!(phoney = malloc(sizeof(int) * i+1)))
         return NC_ENOMEM;
      for (j=0; j<i+1; j++)
         phoney[j] = -99;
      data[i].p = phoney;
      data[i].len = i+1;
   }

   printf("*** Checking simple HDF5 variable length types...");
   
   /* Open file. */
   if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, 
                           H5P_DEFAULT)) < 0) ERR;
   if ((grpid = H5Gcreate(fileid, "grp1", 0)) < 0) ERR;

   /* Create VLEN type. */
   if ((typeid =  H5Tvlen_create(H5T_NATIVE_INT)) < 0) ERR;

   /* Although it's a vlen of ints, the size is rouned up to 8. */
   if (!(size = H5Tget_size(typeid))) ERR;
   if (size < 8) ERR;

   /* Write an attribute of this vlen type. */
   if ((spaceid = H5Screate_simple(1, dims, NULL)) < 0) ERR;
   if ((attid = H5Acreate(grpid, ATT_NAME, typeid, spaceid, 
                          H5P_DEFAULT)) < 0) ERR;
   if (H5Awrite(attid, typeid, data) < 0) ERR;
   if (H5Aclose(attid) < 0) ERR;
   if (H5Tclose(typeid) < 0) ERR;
   if (H5Gclose(grpid) < 0) ERR;
   if (H5Fclose(fileid) < 0) ERR;

   SUMMARIZE_ERR;
   printf("*** Checking array of compound holding a vlen...");
   {
      hid_t vlen_typeid, compound_typeid, spaceid, datasetid;
      struct sea_sounding
      {
            int sounding_no;
            hvl_t temp_vl;
      } data[DIM1_LEN];
      float *phoney;
      int i, j;
      
      /* Create phoney data. */
      for (i=0; i<DIM1_LEN; i++)
      {
         if (!(phoney = malloc(sizeof(float) * i+1)))
            return NC_ENOMEM;
         for (j=0; j<i+1; j++)
            phoney[j] = 23.5 - j;
         data[i].temp_vl.p = phoney;
         data[i].temp_vl.len = i+1;
      }

      /* Create file. */
      if ((fileid = H5Fcreate(FILE_NAME, H5F_ACC_TRUNC, H5P_DEFAULT, 
                              H5P_DEFAULT)) < 0) ERR;
      if ((grpid = H5Gcreate(fileid, "grp1", 0)) < 0) ERR;
      
      /* Create VLEN type. */
      if ((vlen_typeid =  H5Tvlen_create(H5T_NATIVE_FLOAT)) < 0) ERR;

      /* Create a compound type that holds the vlen type. */
      if ((compound_typeid = H5Tcreate(H5T_COMPOUND, 
                                       sizeof(struct sea_sounding))) < 0) ERR;
      if (H5Tinsert(compound_typeid, "sounding_no", HOFFSET(struct 
sea_sounding, sounding_no), 
                    H5T_NATIVE_INT) < 0) ERR;
      if (H5Tinsert(compound_typeid, "temp_vl", HOFFSET(struct sea_sounding, 
temp_vl), 
                    vlen_typeid) < 0) ERR;
      if (H5Tcommit(grpid, "sea_sounding_type", compound_typeid) < 0) ERR;

      if ((spaceid = H5Screate_simple(1, dims, NULL)) < 0) ERR;
      if ((datasetid = H5Dcreate(grpid, "sea_sounding_dataset", 
compound_typeid, 
                                 spaceid, H5P_DEFAULT)) < 0) ERR;
      if (H5Dwrite(datasetid, compound_typeid, H5S_ALL, H5S_ALL, H5P_DEFAULT, 
                   data) < 0) ERR;

      if (H5Dclose(datasetid) < 0) ERR;
      if (H5Tclose(compound_typeid) < 0) ERR;
      if (H5Tclose(vlen_typeid) < 0) ERR;
      if (H5Sclose(spaceid) < 0) ERR;
      if (H5Gclose(grpid) < 0) ERR;
      if (H5Fclose(fileid) < 0) ERR;
   }

   SUMMARIZE_ERR;


   /* Print out our number of errors, if any, and exit badly. */
   if (total_err)
   {
      printf("%d errors detected! Sorry!\n", total_err);
      return 2;
   }
   
   printf("*** Tests successful!\n");
   return 0;
}


-- 
Ed Hartnett  -- ed@xxxxxxxxxxxxxxxx

• Follow-Ups:
  • Re: h5dump problem with compound type containing vlen...
    • From: Pedro Vicente Nunes